{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T17:54:41Z","timestamp":1785779681255,"version":"3.56.0"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T00:00:00Z","timestamp":1771459200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100014254","name":"Soci\u00e9t\u00e9 Fran\u00e7aise de Pathologie Infectieuse de Langue Fran\u00e7aise","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100014254","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002915","name":"Fondation pour la Recherche m\u00e9dicale","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002915","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Among kidney transplant recipients (KTRs) with BK polyomavirus (BKPyV)\u2013associated nephropathy (BKPyVN), the dynamics of BKPyV replication are not well established. We aim to investigate BKPyV genetic diversity and evolution following kidney transplant.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We retrospectively analyzed 32 KTRs with a biopsy-proven diagnosis of BKPyVN. Stored plasma and kidney biopsies were tested for BKPyV viral load, and BKPyV whole genome sequencing was performed on BKPyV-positive samples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>A total of 104 samples positive for BKPyV DNA detection were sequenced, among which 83 were included in the analysis. BKPyV-I was the most frequent genotype detected, followed by BKPyV-IVc2 and BKPyV-II. At BKPyVN diagnosis (median [IQR], 12 [8\u201317] months posttransplant), whole genome sequencing identified the same BKPyV subtype in the plasma and kidney biopsy for all patients but one. Alignment of BKPyV consensus sequences between the 2 compartments at the time of BKPyVN showed similarity &amp;gt;99% but identified single-nucleotide polymorphisms in 13 of 23 cases, including 25% APOBEC-associated mutations. Among the 16 KTRs with \u22652 consecutive BKPyV-positive samples available for analysis, consensus sequence showed a different BKPyV subtype in pre-BKPyVN kidney biopsies as compared with BKPyVN in 9 patients. Before BKPyVN diagnosis, minority variants on the VP1 sequence were identified in 10 of 11 kidney biopsy samples and 5 of 10 plasma samples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Among KTRs with BKPyVN, we show that BKPyV viral populations change over time, with the coexistence of several viral populations in early samples as compared with BKPyVN, as a result of APOBEC-mediated editing and replication-driven diversification within the kidney allograft.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/infdis\/jiag108","type":"journal-article","created":{"date-parts":[[2026,2,15]],"date-time":"2026-02-15T12:32:25Z","timestamp":1771158745000},"page":"64-73","source":"Crossref","is-referenced-by-count":0,"title":["BK Polyomavirus Genetic Diversity and Evolution in Kidney Transplant Recipients With Viral Nephropathy According to Whole Genome Sequencing"],"prefix":"10.1093","volume":"234","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7247-3358","authenticated-orcid":false,"given":"Julien","family":"Gras","sequence":"first","affiliation":[{"name":"Infectious Disease Department, APHP Saint-Louis Hospital"},{"name":"INSERM UMR 1342, Biology and Pathogenesis of Viral Infections Team, Saint Louis Research Institute"},{"name":"Universit\u00e9 Paris Cit\u00e9"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie Laure","family":"Nere","sequence":"additional","affiliation":[{"name":"Virology Department, APHP Saint-Louis Hospital"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julien","family":"Robert","sequence":"additional","affiliation":[{"name":"Bioinformatics Department, APHP Saint-Louis Hospital"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Louis","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9"},{"name":"Nephrology and Kidney Transplant Department, APHP Saint-Louis Hospital"},{"name":"INSERM, PARCC, Paris Institute for Transplantation and Organ Regeneration"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie No\u00eblle","family":"Peraldi","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9"},{"name":"Nephrology and Kidney Transplant Department, APHP Necker Hospital"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda","family":"Feghoul","sequence":"additional","affiliation":[{"name":"Virology Department, APHP Saint-Louis Hospital"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00e9r\u00f4me","family":"Verine","sequence":"additional","affiliation":[{"name":"Pathology Department, APHP Saint-Louis Hospital , Paris ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali","family":"Amara","sequence":"additional","affiliation":[{"name":"INSERM UMR 1342, Biology and Pathogenesis of Viral Infections Team, Saint Louis Research Institute"},{"name":"Universit\u00e9 Paris Cit\u00e9"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carmen","family":"Lefaucheur","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9"},{"name":"Nephrology and Kidney Transplant Department, APHP Saint-Louis Hospital"},{"name":"INSERM, PARCC, Paris Institute for Transplantation and Organ Regeneration"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean Michel","family":"Molina","sequence":"additional","affiliation":[{"name":"Infectious Disease Department, APHP Saint-Louis Hospital"},{"name":"INSERM UMR 1342, Biology and Pathogenesis of Viral Infections Team, Saint Louis Research Institute"},{"name":"Universit\u00e9 Paris Cit\u00e9"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6081-7993","authenticated-orcid":false,"given":"Constance","family":"Delaugerre","sequence":"additional","affiliation":[{"name":"INSERM UMR 1342, Biology and Pathogenesis of Viral Infections Team, Saint Louis Research Institute"},{"name":"Universit\u00e9 Paris Cit\u00e9"},{"name":"Virology Department, APHP Saint-Louis Hospital"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7985-6132","authenticated-orcid":false,"given":"Maud","family":"Salmona","sequence":"additional","affiliation":[{"name":"INSERM UMR 1342, Biology and Pathogenesis of Viral Infections Team, Saint Louis Research Institute"},{"name":"Universit\u00e9 Paris Cit\u00e9"},{"name":"Virology Department, APHP Saint-Louis 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